/// <summary>
/// Enumerate all document peptides. If a library peptide already exists in the
/// current document, update the transition groups for that document peptide and
/// remove the peptide from the list to add.
/// </summary>
/// <param name="document">The starting document</param>
/// <param name="dictCopy">A dictionary of peptides to peptide matches. All added
/// peptides are removed</param>
/// <param name="toPath">Currently selected path.</param>
/// <param name="selectedPath">Selected path after the nodes have been added</param>
/// <returns>A new document with precursors for existing petides added</returns>
private SrmDocument UpdateExistingPeptides(SrmDocument document,
Dictionary <PeptideSequenceModKey, PeptideMatch> dictCopy,
IdentityPath toPath, out IdentityPath selectedPath)
{
selectedPath = toPath;
IList <DocNode> nodePepGroups = new List <DocNode>();
var keysAddedWithoutMatch = new
SortedDictionary <PeptideSequenceModKey, PeptideMatch>();
foreach (PeptideGroupDocNode nodePepGroup in document.MoleculeGroups)
{
IList <DocNode> nodePeps = new List <DocNode>();
foreach (PeptideDocNode nodePep in nodePepGroup.Children)
{
var key = nodePep.SequenceKey;
PeptideMatch peptideMatch;
// If this peptide is not in our list of peptides to add,
// or if we are in a peptide list and this peptide has been matched to protein(s),
// then we don't touch this particular node.
if (!dictCopy.TryGetValue(key, out peptideMatch) ||
(nodePepGroup.IsPeptideList &&
(peptideMatch.Proteins != null && peptideMatch.Proteins.Any())))
{
nodePeps.Add(nodePep);
if (keysAddedWithoutMatch.ContainsKey(key))
{
keysAddedWithoutMatch.Add(key, new PeptideMatch(null, null, false));
}
}
else
{
var proteinName = nodePepGroup.PeptideGroup.Name;
int indexProtein = -1;
if (peptideMatch.Proteins != null)
{
indexProtein =
peptideMatch.Proteins.IndexOf(protein => Equals(protein.ProteinMetadata.Name, proteinName));
// If the user has opted to filter duplicate peptides, remove this peptide from the list to
// add and continue.
if (FilterMultipleProteinMatches == BackgroundProteome.DuplicateProteinsFilter.NoDuplicates && peptideMatch.Proteins.Count > 1)
{
dictCopy.Remove(key);
nodePeps.Add(nodePep);
continue;
}
// [1] If this protein is not the first match, and the user has opted to add only the first occurence,
// [2] or if this protein is not one of the matches, and [2a] we are either not in a peptide list
// [2b] or the user has opted to filter unmatched peptides, ignore this particular node.
if ((indexProtein > 0 && FilterMultipleProteinMatches == BackgroundProteome.DuplicateProteinsFilter.FirstOccurence) ||
(indexProtein == -1 &&
(!nodePepGroup.IsPeptideList || !Properties.Settings.Default.LibraryPeptidesAddUnmatched)))
{
nodePeps.Add(nodePep);
continue;
}
}
// Update the children of the peptide in the document to include the charge state of the peptide we are adding.
PeptideDocNode nodePepMatch = peptideMatch.NodePep;
PeptideDocNode nodePepSettings = null;
var newChildren = nodePep.Children.ToList();
Identity nodeGroupChargeId = newChildren.Count > 0 ? newChildren[0].Id : null;
foreach (TransitionGroupDocNode nodeGroup in nodePepMatch.Children)
{
var chargeGroup = nodeGroup.TransitionGroup.PrecursorAdduct;
if (nodePep.HasChildCharge(chargeGroup))
{
SkippedPeptideCount++;
}
else
{
if (nodePepSettings == null)
{
nodePepSettings = nodePepMatch.ChangeSettings(document.Settings, SrmSettingsDiff.ALL);
}
TransitionGroupDocNode nodeGroupCharge = (TransitionGroupDocNode)nodePepSettings.FindNode(nodeGroup.TransitionGroup);
if (nodeGroupCharge == null)
{
continue;
}
if (peptideMatch.Proteins != null && peptideMatch.Proteins.Count > 1)
{
// If we may be adding this specific node to the document more than once, create a copy of it so that
// we don't have two nodes with the same global id.
nodeGroupCharge = (TransitionGroupDocNode)nodeGroupCharge.CopyId();
nodeGroupCharge = (TransitionGroupDocNode)nodeGroupCharge.ChangeChildren(
nodeGroupCharge.Children.ToList().ConvertAll(child => child.CopyId()));
}
nodeGroupChargeId = nodeGroupCharge.Id;
newChildren.Add(nodeGroupCharge);
}
}
// Sort the new peptide children.
newChildren.Sort(Peptide.CompareGroups);
var nodePepAdd = nodePep.ChangeChildrenChecked(newChildren);
// If we have changed the children, need to set automanage children to false.
if (nodePep.AutoManageChildren && !ReferenceEquals(nodePep, nodePepAdd))
{
nodePepAdd = nodePepAdd.ChangeAutoManageChildren(false);
}
// Change the selected path.
if (PeptideMatches.Count == 1)
{
selectedPath = nodeGroupChargeId == null
? new IdentityPath(new[] { nodePepGroup.Id, nodePepAdd.Id })
: new IdentityPath(new[] { nodePepGroup.Id, nodePepAdd.Id, nodeGroupChargeId });
}
nodePeps.Add(nodePepAdd);
// Remove this peptide from the list of peptides we need to add to the document
dictCopy.Remove(key);
if (peptideMatch.Proteins != null)
{
if (indexProtein != -1)
{
// Remove this protein from the list of proteins associated with the peptide.
peptideMatch.Proteins.RemoveAt(indexProtein);
}
// If this peptide has not yet been added to all matched proteins,
// put it back in the list of peptides to add.
if (peptideMatch.Proteins.Count != 0 && FilterMultipleProteinMatches != BackgroundProteome.DuplicateProteinsFilter.FirstOccurence)
{
dictCopy.Add(key, peptideMatch);
}
}
}
}
nodePepGroups.Add(nodePepGroup.ChangeChildrenChecked(nodePeps));
}
return((SrmDocument)document.ChangeChildrenChecked(nodePepGroups));
}